[Biopython-dev] BOSC 2012 - Biopython Update

[Eric Talevich]

On Thu, Apr 12, 2012 at 12:01 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hello all,
>
> The BOSC abstract deadline (tomorrow) has rather crept up on me,
> despite Nomi's reminder emails (My excuse is I've been thinking
> more about GSoC!). For anyone thinking of submitting a talk, the
> abstract limit is just a page - see:
> http://www.open-bio.org/wiki/BOSC_2012
>
> I'm hoping to attend BOSC, but will probably not be at ISMB 2012.
> I'd be delighted for another Biopython developer to give the project
> update talk (and as in previous years, we'll help out with the abstract,
> slides, etc). Anyone interested? Giving a talk can be very helpful in
> getting travel funding ;)
>
> I know Eric might be a candidate as he will be in Long Beach
> (congratulations on getting your ISMB poster accepted Eric!).
>
> Note that dedicated "Bioinformatics Open Source Project Updates"
> track is new this year. The talks are likely to be at the shorter end of
> the talk length range specified (i.e. closer to 5 minutes than 20 mins)
> but that will partly depend on quite how full the final schedule turns
> out to be.
>
> The idea (speaking with my BOSC hat on) with the update talks is
> to try to highlight what is new and exciting, with only a minimal
> introduction for the higher profile projects - most of the audience
> will know roughly what BioPerl etc are, and won't be interested
> to hear it again ;)
>
> So for the Biopython talk we'd probably want to cover things like
> GSoC, work with PyPy and Python3, major new functionality, any
> Biopython papers, etc, and a bit on future plans. The talk should be
> short but sweet :)
>
> Regards,
>
> Peter


OK, here are some potential talking points I scraped from past announcements:

* SeqIO.index_db:
Introduced v.1.57 (Apr 2011), with improvements since then. Ideas to
carry the index_db concept to other modules.

* Installation improvements:
pip support (v.1.57); easy_install will automatically handle the numpy
dependency (v.1.59, Feb '12)

* Portability:
Python 3 compatibility (except for a couple C extension modules);
still supporting Jython; now mostly supporting Pypy (except for
modules that use numpy or C extensions)

* Merged Brandon Invergo's independent project pypaml under
Bio.Phylo.PAML ((v.1.58, Aug '11). With SeqIO's new sequential Phylip
support (v.1.59) and the existing support for phylogeny I/O under
Phylo, we can now easily assemble and run complete workflows involving
PAML.
(Similarly for PhyML, with SeqIO's "phylip-relaxed" and
Bio.Phylo.Applications.PhymlCommandline.)

* GenomeDiagram improvements:
New, pretty features. Eye candy for the slides.

* TogoWS

* Next release & future plans:
- Restored mmCIF support, via Lenna Peterson, a prospective GSoC student
- Brad's GFF parser
- Deeper future: see the other mailing list thread

* GSoC 2011 results:
- Mikael Trellet -- Interface
- Michele Silva -- Mocapy++ Python module; also ported two
applications to Biopython
- Justinas D. -- Python-based extension system for Mocapy++

* Summer of Struct:
João and Eric are working to refactor and merge the vast amount of
Bio.PDB-related code produced during previous GSoCs. (Includes a
planned SeqIO-style API for structures in PDB, mmCIF and PBDML
formats.) Improvements have been trickling in since the last BOSC;
here comes the flood.